BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818893.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,325,451 number of mapped reads = 1,296,364 (97.81%) number of supplementary alignments = 19,967 (1.51%) number of secondary alignments = 0 number of mapped bases = 119,915,767 bp number of sequenced bases = 119,837,772 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 226,757 duplication rate = 14.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2288 >>>>>>> ACTG content number of A's = 34,206,485 bp (28.54%) number of C's = 25,205,093 bp (21.03%) number of T's = 34,365,400 bp (28.68%) number of G's = 26,058,898 bp (21.75%) number of N's = 1,896 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 750,610 number of insertions = 19,018 mapped reads with insertion percentage = 1.42% number of deletions = 39,299 mapped reads with deletion percentage = 2.96% homopolymer indels = 39.65% >>>>>>> Coverage mean coverageData = 0.0387X std coverageData = 0.5283X There is a 2.9% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11355300 0.04555776011486848 0.7865341139456212 chr2 243199373 9141908 0.037590179149022726 0.8033267041893161 chr3 198022430 7337079 0.037051757217604085 0.24155848504621694 chr4 191154276 6044648 0.031621829898275465 0.31816713480645686 chr5 180915260 5301036 0.029301209859245704 0.23414451626737617 chr6 171115067 5917894 0.034584295256711674 0.2547366035985023 chr7 159138663 10766325 0.06765373540935178 1.1194791254484924 chr8 146364022 10356172 0.0707562682310001 0.4114088896925835 chr9 141213431 4409116 0.03122306404409932 0.4086114957175796 chr10 135534747 5697762 0.04203912373850523 0.7504352565675153 chr11 135006516 5293956 0.03921259622757764 0.304626063261234 chr12 133851895 4611272 0.034450554472912016 0.23570293575632015 chr13 115169878 3613331 0.03137392400467768 0.21974529609922044 chr14 107349540 3497708 0.03258242187157952 0.25488782339286864 chr15 102531392 3302283 0.03220753113348934 0.22747428050206553 chr16 90354753 3012879 0.03334499735725026 0.5507448483968532 chr17 81195210 2931758 0.03610752407685133 0.31212454333862444 chr18 78077248 2313070 0.029625403805216086 0.4790049433868852 chr19 59128983 2100282 0.035520347102875084 0.6371174797696819 chr20 63025520 4872127 0.07730403493695887 0.3785904856817138 chr21 48129895 1165223 0.024209963474883956 0.25221060061099393 chr22 51304566 1098514 0.021411622505490058 0.21201352922941488 chrMT 16571 377992 22.810451994448133 14.346650959643828 chrX 155270560 4925614 0.0317227811891707 0.26704780693435765 chrY 59373566 472518 0.007958390102423695 0.6309103901760389